Entity-relation diagram of the DNA Module V2.0

Overview

DNA extractions

ER diagram Package "DNA extractions"

Main package of the DNA Module, related to many other packages.
The main table is dnabanknumbers with several related list tables. The table people is connected to the dna extractions via three IDs: ExtractionStaff, Provided_By and AmplificationStaff.

Main tables:

dnabanknumbers

people

List tables:

dnatype

relationdna_voucher

tissue

preservation

extractionmethod

purification

degradation

images

Related packages:

Amplifications

Locations Aliquots/stock

Specimen cache

Requests

Molecular publications

Log tables

Specimen data providers

ER diagram package “Specimen data providers”

List of all connected specimen data providers (GBIF compliant databases). More than one dataset per provider is possible. The required schema and provider software is recorded by ID_Schema. The Specimen Tool is predefined with ID_Dataset = '1'. The Wrapper urls of both the Specimen Tool and the DNA data are left empty until definition via the Configuration Tool.

Main table:

dataset

Related packages:

Specimen cache

Specimen Tool

Specimen cache

ER diagram package “Specimen cache”

A few specimen parameters have to be recorded within the DNA Module database to enable search for exisiting taxa in the DNA database et cetera.
The specimen data are recorded in four tables to get all available determinations and higher taxa. One specimen can be connected to several DNA extractions.

Main table:

cachecollection

Related packages:

Specimen data providers

DNA extractions

Locations stock/aliquots

ER diagram package “Location stock/aliquots”

This package records the location and volumes of all aliquot and stock samples in the freezers. The information in this package is completely internal and help to find out easily which samples can be send to customers and which have to be extracted.

Main tables:

aliquots

location_stock

List tables:

aliquots_box

aliquots_fridge

aliquots_rack

stock_box

stock_fridge

stock_rack

Related packages:

DNA extraction

Customer requests

Publications

UPDATE of docu required.
This package allows to associate any publications to DNA or samples and specimen data. It should not be a complete substitute for a literature management software.

Main table:

reference

Related packages:

DNA extractions

Specimen Tool

Sequence data

Sequence data

ER diagram package “Sequence data”

This package is for management of GenBank Accession Numbers, BOLD process IDs and Amplifications in general. More tables have been modelled for future management of raw sequence data, including primers, references, cloning etc. The frontend for this tables will be ready for use until end of 2011. For now only GenBank/BOLD accessions and Amplifications can be administrated.

Main tables:

amplifications

sequencing

List tables:

geneticlocus

primer

cloningmethod

sequencingmethod

Related packages:

DNA extractions

Molecular publications

Customer requests

ER diagram package “Customer requests”

This package includes management of all customer requests respectively orders. Since way of administer payments depends on institution this package is for the lab site only.

Main table:

request

Related packages:

Location stock/aliquots

DNA extractions

Specimen Tool

ER diagram package “Specimen Tool”

This is a stand-alone package that interact with the DNA Module via wrapper. It has been developed for specimen data that are not available via GBIF. Furthermore external duplicates or similiar relevant objects can be associated.

Main table:

sptoolcollection

List tables:

basisofrecordspecimen

countryisocode

prevalentaspect

seasandoceans

sex

slope

specimentype

Related packages:

Specimen data providers

Table descriptions

All of the following information is stored directly in the tables, including the description and comments. Wiki-syntax is generated by running a php script. Last update: 2015-02-08